- Refinements on PSU section:
[...]So you want to feed the FPGA's 2.5V rail through the MSP's built-in LDO? Doesn't sound good

Of course not. There are two 2.5V supplies in the PSU design:
VCC: Fed by the 3.3V LDO in the MSP430. Powers the MSP430 and nothing else.
VCCIO: Fed by the +12V connector. Powers the VCCio rail of both FPGAs.